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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbc:B3207, See in JSmolMgRNA representative site for type 3PO-RO-3BO Click on the image to toggle views


Site type: 3Pout·Rout·3Bout

Schematic drawing for
3Pout·Rout·3Bout
MgRNA type 3PO-RO-3BO
List of all 33 Mg2+ binding sites with the site type 3Pout·Rout·3Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2aw4 B2956 3Pout·Rout·3Bout B3256, B3257, B3258, B3259, B3260, B3261 A:B1253, A:B582, G:B583 C:B1251 G:B583, C:B584, A:B582
2awb B2939 3Pout·Rout·3Bout B3184, B3185, B3186, B3187, B3188, B3189 A:B447, A:B28, U:B29 A:B447 G:B473, U:B29, G:B474
2qam B3302 3Pout·Rout·3Bout B3857, B3858, B3859, B3860, B3861, B3862 A:B1253, A:B582, G:B583 C:B1251 G:B583, C:B584, A:B582
2qao B3207 3Pout·Rout·3Bout B3789, B3790, B3791, B3792, B3793, B3794 A:B447, A:B28, U:B29 A:B447 U:B29, G:B473, G:B474
2qbc B3207 3Pout·Rout·3Bout B3789, B3790, B3791, B3792, B3793, B3794 A:B447, A:B28, U:B29 A:B447 U:B29, G:B473, G:B474
2qbc B3320 3Pout·Rout·3Bout B3881, B3882, B3883, B3884, B3885, B3886 A:B582, G:B583, A:B1253 C:B1251 A:B582, G:B583, G:B585
2qox B2959 3Pout·Rout·3Bout B3277, B3278, B3279, B3280, B3281, B3282 A:B582, G:B583, A:B1253 C:B1251 C:B584, G:B585, A:B582
3i1t A2920 3Pout·Rout·3Bout A3123, A3124, A3125, A3126, A3127, A3128 A:A582, A:A1253, G:A583 C:A1251 C:A584, A:A582, G:A583
3i20 A2905 3Pout·Rout·3Bout A3046, A3047, A3048, A3049, A3050, A3051 U:A29, A:A28, A:A447 A:A447 G:A473, G:A474, U:A29
3ofq A2921 3Pout·Rout·3Bout A3120, A3121, A3122, A3123, A3124, A3125 A:A582, A:A1253, G:A583 C:A1251 G:A583, G:A585, A:A582
3ofq A2906 3Pout·Rout·3Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A28, A:A447 A:A447 G:A473, U:A29, G:A30
3og0 A3026 3Pout·Rout·3Bout A3593, A3594, A3595, A3596, A3597, A3598 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568, A:A821
3v25 A3289 3Pout·Rout·3Bout A3712, A3713, A3714, A3715 G:A570, A:A973, U:A569 G:A972 U:A568, A:A820, A:A821
3v27 A3627 3Pout·Rout·3Bout A5218, A5219, A5220, A5221, A5222, A5223 A:A1609, C:A1617, G:A1619 C:A1617 G:A1613, G:A1619, G:A1620
3v2d A3693 3Pout·Rout·3Bout A5663, A5664, A5665, A5666, A5667, A5668 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821, U:A568
4bpe A5046 3Pout·Rout·3Bout A2075, A2078, A2081, A2082, A2083, A2314 A:A437, A:A448, G:A449 C:A436 G:A449, G:A450, A:A448
4bpn A5069 3Pout·Rout·3Bout A6549, A6550, A6551, A6552, A6553, A6555 G:A1148, C:A1428, C:A1149 C:A1427 G:A1172, A:A1174, U:A1159
4bpn A5046 3Pout·Rout·3Bout A6131, A6132, A6133, A6134, A6135, A6136 A:A437, A:A448, G:A449 C:A436 A:A448, G:A449, G:A450
4bpo A5046 3Pout·Rout·3Bout A2073, A2076, A2079, A2080, A2081, A2410 A:A437, A:A448, G:A449 C:A436 G:A449, G:A450, A:A448
4bpp A5046 3Pout·Rout·3Bout A7747, A7748, A7749, A7750, A7751, A7752 A:A437, A:A448, G:A449 C:A436 A:A448, G:A449, G:A450
4dha A3646 3Pout·Rout·3Bout A4527, A4528, A4529, A4530, A4531 A:A1609, C:A1617, G:A1619 C:A1617 G:A1613, G:A1619, G:A1620
4gar A3016 3Pout·Rout·3Bout A3284, A3285, A3286, A3287, A3288, A3289 A:A582, A:A1253, G:A583 C:A1251 C:A584, G:A585, G:A583
4nvx A3361 3Pout·Rout·3Bout A4314, A4315, A4316, A4317, A4318, A4319 G:A570, A:A973, U:A569 G:A972 A:A821, A:A820, U:A568
4nvz A3479 3Pout·Rout·3Bout A4536, A4537, A4538, A4539, A4540 A:A1655, C:A1663, G:A1665 C:A1663 G:A1665, G:A1659, G:A1666
4nw1 A3355 3Pout·Rout·3Bout A4313, A4314, A4315, A4316, A4317, A4318 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821, U:A568

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"		 Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen 		cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform 		Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>